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Recent experimental studies have highlighted a central role of cell rearrangements in the formation of angiogenic networks. Our model accounts for this phenomenon via the heterogeneous response of ECs to their microenvironment. These cell rearrangements, in turn, dynamically remodel the local environment. The model reproduces characteristic features of angiogenic sprouting that include branching, chemotactic sensitivity, the brush border effect, and cell mixing. These properties, rather than being hardwired into the model, emerge naturally from the gene expression patterns of individual cells. After calibrating and validating our model against experimental data, we use it to predict how the structure of the vascular network changes as the baseline gene expression levels of the VEGF-Delta-Notch pathway, and the composition of the extracellular environment, vary. In order to investigate the impact of cell rearrangements on the vascular network structure, we introduce the mixing measure, a scalar metric that quantifies cell mixing as the vascular network grows. We calculate the mixing measure for the simulated vascular networks generated by ECs of different lineages (wild type cells and mutant cells with impaired expression of a specific receptor). Our results show that the time evolution of the mixing measure is directly correlated to the generic features of the vascular branching pattern, thus, supporting the hypothesis that cell rearrangements play an essential role in sprouting angiogenesis. Furthermore, we predict that lower cell rearrangement leads to an imbalance between branching and sprout elongation. Since the computation of this statistic requires only individual cell trajectories, it can be computed for networks generated in biological experiments, making it a potential biomarker for pathological angiogenesis.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008055","type":"journal-article","created":{"date-parts":[[2021,1,7]],"date-time":"2021-01-07T18:39:13Z","timestamp":1610044753000},"page":"e1008055","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":43,"title":["A multiscale model of complex endothelial cell dynamics in early angiogenesis"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1771-1987","authenticated-orcid":true,"given":"Daria","family":"Stepanova","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1771-5910","authenticated-orcid":true,"given":"Helen 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Dynamical Analysis Predicts Partial Tip\/Stalk Patterning States Arise during Angiogenesis","volume":"11","author":"L Venkatraman","year":"2016","journal-title":"PLoS One"},{"issue":"45","key":"pcbi.1008055.ref078","doi-asserted-by":"crossref","first-page":"18144","DOI":"10.1073\/pnas.1318192110","article-title":"MicroRNA-based regulation of epithelial\u2013hybrid\u2013mesenchymal fate determination","volume":"110","author":"M Lu","year":"2013","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"25","key":"pcbi.1008055.ref079","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1098\/rsif.2008.0014","article-title":"Random walk models in biology","volume":"5","author":"EA Codling","year":"2008","journal-title":"Journal of the Royal Society Interface"},{"key":"pcbi.1008055.ref080","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-29488-4","volume-title":"An introduction to kinetic Monte Carlo simulations of surface reactions","author":"APJ 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